The objective of this study was to assess the water collection, treatment, and contamination in Upper and Lower Belén neighborhoods of Iquitos, Peru to address the longstanding prevalence of waterborne disease. Fifty household surveys were performed and 45 water samples were analyzed for fecal coliforms (FC). Most drinking water was untreated at home and negative for FC. Of the FC-positive waters (11.1%), the source was Sedaloreto tap water, the municipally owned water company and treatment facility. No FC-positive samples resulted from residences reporting home treatment. This suggests sufficient sterilization at the point of treatment but contamination within the distribution system or individual homes. Therefore, it is critical to emphasize the importance of home-based treatment until the distribution system can be reliable. Although the prevalence of FC-positive samples were similar in Upper and Lower Belén, residents in Lower Belén remain at increased risk for waterborne disease due to seasonal environmental conditions such as flooding and the lack of home sanitation facilities.